Nick George
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Making a lookup table (LUT) for ImageJ from an existing image

First published: January 5, 2020
Last updated: January 8, 2023

ImageJ lookup tables (LUTs) map integer or floating point pixel values to colors. ImageJ comes with a lot of nice LUTs and there are many available on the internet as well (Christophe Leterrier has excellent ones available here https://github.com/cleterrier/ChrisLUTs). I recently wanted to make my own based on a colormap on an image exported from our microscope (myelin is the blue-ish color below that I wanted to use).

imageJ displaying an image

Creating your own LUT from a reference image

  • Open up the image and switch to your target channel (in this case channel 4).

You can view the raw values of the LUT by clicking Image>Color>Show LUT and clicking "List" on the resulting window.

how to display a LUT in imagej
  • Split the channels so only your channel of interest is showing (Image>Color>Split Channels close all unrelated channels), and save this as a LUT by clicking File>Save As...> LUT.... I saved mine as mylein-test-lut.

saving an image as a LUT in ImageJ
  • Move this file to Fiji.app/luts/ directory.

  • Close and re-open Fiji and you should see your new LUT in the options menu

see your new LUT in the LUTs menu

References